These are the web-services:
auth-token; retrieve an authentication token (for use with the other web-services).
boadicea; calculates risks and mutation carrier probabilities for breast cancer.
ovarian; calculates risks and mutation carrier probabilities for ovarian cancer.
vcf2prs; takes a VCF file and returns a PRS (alpha and z-score) for use in the breast and ovarian cancer web-services.
The following describes auth-token and boadicea.
...
The following examples use the curl command to send requests to each of the web-services.
Obtaining Authentication Token (replace URL with the CanRisk website address):
curl -k 'https://{URL}/auth-token/' \-d '{"username": "XYZ", "password": "ABC"}' \-H "Content-Type: application/json"Running a breast cancer risk calculation with pedigree data as a JSON parameter (replace with the authentication token):
CanRisk v1 formatcurl -k -XPOST -H "Content-Type: application/json" -d '{"mut_freq":"UK","cancer_rates":"UK","user_id":"end_user_id","pedigree_data":"##CanRisk
...
1.0\n##menarche
...
=12\n##oc_use=N\n##mht_use=N\n##BMI=
...
23.
...
01\n##alcohol=
...
44.8\n##height=
...
180.34\n##FamID\tName\tTarget\tIndivID\tFathID\tMothID\tSex\tMZtwin\tDead\tAge\tYob\tBC1\tBC2\tOC\tPRO\tPAN\tAshkn\tBRCA1\tBRCA2\tPALB2\tATM\tCHEK2\
...
tRAD51D\tRAD51C\tBRIP1\tER:PR:HER2:CK14:CK56\
...
nXXXX\
...
tpa\t0\tm21\t0\t0\tM\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0
...
\t0:0\t0:0\t0:0\t0:0\t0:0\t0:0\t0:0\t0:0\t0:0:0:0:0\
...
nXXXX\
...
tma\t0\tf21\t0\t0\tF\t0\t0\
...
t0\
...
t0\
...
t0\t0\t0\t0\t0\t0\
...
t0:
...
0\
...
t0:
...
0\
...
t0:
...
0\
...
t0:
...
0\
...
t0:
...
0\
...
t0:
...
0\
...
t0:
...
0\
...
t0:0\t0:0:0:0:0\
...
nXXXX\
...
tme\t1\tch1\tm21\tf21\tF\t0\t0\
...
t42\
...
t1977\
...
t38\t0\t0\t0\t0\t0\
...
tS:
...
N\
...
tS:
...
N\
...
tS:
...
N\
...
tS:N\t0:0\t0:0\t0:0\t0:0\t0:0:0:0:0\n"}' https://{URL}/boadicea/ -H "Authorization: Token <TOKEN>"
or with a pedigree file POSTed as a formcurl -k -XPOST -F "mut_freq=UK" -F "cancer_rates=UK" -F "user_id=end_user_id" -F "pedigree_data=@/home/xxxx/d10.
...
canrisk" https://{URL}/boadicea/ -H "Authorization: Token <TOKEN>" -H "Accept: application/json"
BOADICEA formatcurl -k -XPOST -H "Content-Type: application/json" \-H 'Authorization: Token <TOKEN>' -H "Accept: application/json" \
-d '{"mut_freq": "UK", "cancer_rates":"UK", "user_id": "end_user_id",
pedigree_data":"BOADICEA import pedigree file format 4.0\nFamID\tName\tTarget\tIndivID\tFathID\tMothID\tSex\tMZtwin\tDead\tAge\tYob\t1stBrCa\t2ndBrCa\tOvCa\tProCa\tPanCa\tAshkn\tBRCA1t\tBRCA1r\tBRCA2t\tBRCA2r\tPALB2t\tPALB2r\tATMt\tATMr\tCHEK2t\tCHEK2r\tER\tPR\tHER2\tCK14\tCK56\nXXX1 \tF1 \t1\t1 \t3 \t2 \tF\t0\t0\t23 \t1993\t21 \t0 \t0 \t0 \t0 \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\nXXX1 \tF2 \t0\t2 \t0 \t0 \tF\t0\t0\t55 \t1961\t0 \t0 \t0 \t0 \t0 \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\nXXX1 \tM2 \t0\t3 \t0 \t0 \tM\t0\t0\t53 \t1963\t0 \t0 \t0 \t0 \t0 \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0"}' https://{URL}/boadicea/Running a ovarian cancer risk calculation with a pedigree file POSTed as a form:
curl -k -XPOST -F "mut_freq=UK" -F "cancer_rates=UK" \-F "user_id=end_user_id" \-F "pedigree_data=@/home/xxx/bwa4_pedigree_data.txt" \https://{URL}/ovarian/ -H 'Authorization: Token <TOKEN>' -H "Accept: application/json"Obtaining a PRS for breast cancer:
curl -k -XPOST -F "bc_prs_reference_file=BCAC_313_PRS.prs" -F "sample_name=SampleA" \-F "vcf_file=@/home/xxx/sample_BCAC_313.vcf" \https://{URL}/vcf2prs/ \-H 'Authorization: Token <TOKEN>' -H "Accept: application/json"
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